2q2t: Difference between revisions

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-[[Image:2q2t.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2q2t", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2q2t|  PDB=2q2t  |  SCENE=  }}
-'''Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick'''
+==Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick==
+<StructureSection load='2q2t' size='340' side='right'caption='[[2q2t]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2q2t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paramecium_bursaria_Chlorella_virus_1 Paramecium bursaria Chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q2T FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2t OCA], [https://pdbe.org/2q2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q2t RCSB], [https://www.ebi.ac.uk/pdbsum/2q2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q2t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O41026_PBCV1 O41026_PBCV1]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/2q2t_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q2t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Chlorella virus DNA ligase, the smallest eukaryotic ligase known, has pluripotent biological activity and an intrinsic nick-sensing function, despite having none of the accessory domains found in cellular ligases. A 2.3-A crystal structure of the Chlorella virus ligase-AMP intermediate bound to duplex DNA containing a 3'-OH-5'-PO4 nick reveals a new mode of DNA envelopment, in which a short surface loop emanating from the OB domain forms a beta-hairpin 'latch' that inserts into the DNA major groove flanking the nick. A network of interactions with the 3'-OH and 5'-PO4 termini in the active site illuminates the DNA adenylylation mechanism and the crucial roles of AMP in nick sensing and catalysis. Addition of a divalent cation triggered nick sealing in crystallo, establishing that the nick complex is a bona fide intermediate in the DNA repair pathway.
-==Overview==
+Structural basis for nick recognition by a minimal pluripotent DNA ligase.,Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S Nat Struct Mol Biol. 2007 Aug;14(8):770-8. Epub 2007 Jul 8. PMID:17618295<ref>PMID:17618295</ref>
-Chlorella virus DNA ligase, the smallest eukaryotic ligase known, has pluripotent biological activity and an intrinsic nick-sensing function, despite having none of the accessory domains found in cellular ligases. A 2.3-A crystal structure of the Chlorella virus ligase-AMP intermediate bound to duplex DNA containing a 3'-OH-5'-PO4 nick reveals a new mode of DNA envelopment, in which a short surface loop emanating from the OB domain forms a beta-hairpin 'latch' that inserts into the DNA major groove flanking the nick. A network of interactions with the 3'-OH and 5'-PO4 termini in the active site illuminates the DNA adenylylation mechanism and the crucial roles of AMP in nick sensing and catalysis. Addition of a divalent cation triggered nick sealing in crystallo, establishing that the nick complex is a bona fide intermediate in the DNA repair pathway.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Q2T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2T OCA].
+</div>
+<div class="pdbe-citations 2q2t" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural basis for nick recognition by a minimal pluripotent DNA ligase., Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S, Nat Struct Mol Biol. 2007 Aug;14(8):770-8. Epub 2007 Jul 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17618295 17618295]
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
-[[Category: Paramecium bursaria chlorella virus 1]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Lima, C D.]]
+__TOC__
-[[Category: Nair, P A.]]
+</StructureSection>
-[[Category: Nandakumar, J.]]
+[[Category: Large Structures]]
-[[Category: Shuman, S.]]
+[[Category: Paramecium bursaria Chlorella virus 1]]
-[[Category: Smith, P.]]
+[[Category: Lima CD]]
-[[Category: Ligase]]
+[[Category: Nair PA]]
-[[Category: Ligase/dna complex]]
+[[Category: Nandakumar J]]
-[[Category: Lysine adenylate]]
+[[Category: Shuman S]]
-[[Category: Protein-dna complex]]
+[[Category: Smith P]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:13:20 2008''